Phylogenetic representations of data shown in Table 1. A. Topology predicted for genes duplicated in ray-finned fish before the divergence of the zebrafish and pufferfish lineages with both copies retained and sequenced in both species. B. Topology predicted for genes duplicated in fish before the divergence of zebrafish and pufferfish but with one copy lost or not sequenced in pufferfish.C. “Out-group topology”: Topology often recovered when a gene/phylogenetic method combination did not produce the topology predicted by the fish-specific genome duplication hypothesis (e.g., “−“ in Table 1). For many genes, we suspect that the recovery of an out-group topology is an artefact produced by Long Branch Attraction (see Discussion). D. Biologically plausible explanation for the out-group topology: Loss of tetrapod orthologs of “basal” fish lineage.
